The present invention relates to optical confinements, methods of preparing and methods of using them for analyzing molecules and/or monitoring chemical reactions. The apparatus and methods embodied in the present invention are particularly useful for high-throughput and low-cost single-molecular analysis.

Claim:

The invention claimed is:

1. A method of characterizing a single nucleic acid molecule, comprising: a) providing the single nucleic acid molecule, wherein the single nucleic acid moleculecomprises a first sequence of contiguous nucleotides; b) performing iterative sequencing of the first sequence of contiguous nucleotides in the single nucleic acid molecule by subjecting the single nucleic acid molecule to a template-directedpolymerization reaction, wherein the iterative sequencing comprises sequencing the first sequence of contiguous nucleotides in the single nucleic acid molecule multiple times during the polymerization reaction, thereby generating multiple reads of thefirst sequence of contiguous nucleotides; and c) analyzing the multiple reads to determine a sequential base composition for the first sequence of contiguous nucleotides, thereby characterizing the single nucleic acid molecule.

2. The method of claim 1, wherein the first sequence of contiguous nucleotides is present once in the nucleic acid.

3. The method of claim 1, wherein the first sequence of contiguous nucleotides is present at least two to 100 times in the nucleic acid.

4. The method of claim 1, wherein the single nucleic acid molecule is a linear concatemer.

5. The method of claim 1, wherein the single nucleic acid molecule is circular.

6. The method of claim 1, wherein the multiple reads are generated in step b) in real time during the template-directed polymerization reaction.

7. The method of claim 1, wherein the multiple reads are generated at a speed of at least one base pair per second.

9. The method of claim 6, wherein a polymerase enzyme performing the template-directed polymerization reaction is a modified or unmodified .PHI.29 DNA polymerase.

10. The method of claim 1, wherein the method is performed in the presence of a plurality of types of nucleotides or nucleotide analogs.

11. The method of claim 10, wherein each of the plurality of types of nucleotides or nucleotide analogs comprises a label.

12. The method of claim 11, wherein the label is attached at a base, sugar moiety, alpha phosphate, beta phosphate, or terminal phosphate of the nucleotides or nucleotide analogs.

13. The method of claim 11, wherein the label is a fluorescence resonance energy transfer donor or acceptor.

14. The method of claim 10, wherein the nucleotides or nucleotide analogs comprise a phosphate moiety selected from the group consisting of monophosphate, diphosphate, triphosphate, tetraphosphate, pentaphosphate, and hexaphosphate, and furthercomprise a label on a terminal phosphate of the phosphate moiety.

15. The method of claim 10, wherein each type of the plurality of types of nucleotides or nucleotide analogs has a different label that renders it distinguishable from every other type of the plurality of types during the generating of themultiple reads, and wherein the generating comprises identifying each type of the plurality of types of nucleotides or nucleotide analogs based upon the different label.

16. The method of claim 1, wherein the single nucleic acid molecule is covalently or noncovalently attached to a support.

17. The method of claim 16, wherein the single nucleic acid molecule is attached to the support via interaction with at least one of the group consisting of a streptavidin/biotin linkage, an avidin/biotin linkage, a carbamate linkage, an esterlinkage, an amide, a thiolester, an (N)-functionalized thiourea, a functionalized maleimide, an amino, a disulfide, an amide, a hydrazone linkage, an antibody, a silyl moiety, and an enzyme bound to the substrate.

18. The method of claim 1, wherein the generating takes place in an optical confinement.

19. The method of claim 18, wherein the generating takes place in a zero-mode waveguide.

20. The method of claim 18, wherein the optical confinement contains a single complex comprising the single nucleic acid molecule.

21. The method of claim 20, wherein the single complex further comprises a polymerase.

22. The method of claim 18, wherein the generating takes place in an array of optical confinements.

23. The method of claim 22, wherein the array of optical confinements has a density on a support exceeding 4.times.10.sup.4 confinements per mm.sup.2.

24. The method of claim 22, wherein the array of optical confinements has a density on a support exceeding 10.sup.5 confinements per mm.sup.2.

25. The method of claim 1, wherein the template-directed polymerization reaction comprises use of a modified or unmodified .PHI.29 DNA polymerase.